SCENIC: Generating gene-regulatory networks (streaming version)

Loads the genes in as chunks to avoid high memory pressure.

Usage

rs_scenic_grn_streaming(
  f_path_genes,
  cell_indices,
  gene_indices,
  tf_indices,
  scenic_params,
  seed,
  verbose
)

Arguments

f_path_genes

Path to the counts_genes.bin file.

cell_indices

Integer vector. 0-indexed(!) positions of cells to include in the analysis

gene_indices

Integer vector. 0-indexed(!) positions of the genes to include.

tf_indices

Integer vector. 0-indexed(!) positions of the TF predictor variables to use in the generation of the regression learners.

scenic_params

Named list. Contains all of the parameters need for SCENIC.

seed

Integer. Controls reproducibility of the function.

verbose

Boolean. Controls the verbosity of the function.

Value

A gene x TF importance matrix